Many times we'll run tests in an attempt to compare two things. Maybe we're comparing our performance against that of a "comparable" (read: competitor's) product. Maybe we're comparing new software on cheaper hardware to see if we've lost speed in a "comparable" (read: offers our customers about the same thing) configuration. These comparisons are completely legitimate, but we need to be a bit careful with them.
Maybe we do want to compare apples to oranges. After all, they're both fruits. They're both round. They both come from trees. They both have seeds on the inside.
Apples are like oranges, if the thing we're trying to compare is seed location.
Maybe, though, we want to compare apples to strawberries. After all, apples and strawberries are both red. Perhaps we're most interested in making sure that whatever we compare is red. Or perhaps it's that they both have stems that come with the fruit. Maybe it's fruits with edible skin.